def tearDown(self):
#return
dnames = dirutil.walkdirs("childdir",1,1)
for dname in dnames:
shutil.rmtree(dname)
fnames = dirutil.walkfiles("childdir",1,1)
for fname in fnames:
os.remove(fname)
def test_dfe_tool(self):
import subprocess
os.chdir("archive/GaAs_defects_AsGa_recipe_defects_20131125T220427/dfe_ingredient")
mydfetest=subprocess.Popen(["mast_defect_formation_energy dfe_input.txt"],shell=True)
mydfetest.wait()
os.chdir(testdir)
compare_walk = dirutil.walkfiles("compare_results")
compare_walk.remove("compare_results/__init__.py")
compare_walk.remove("compare_results/__init__.pyc")
res_walk = dirutil.walkfiles("archive/GaAs_defects_AsGa_recipe_defects_20131125T220427/dfe_ingredient/dfe_results")
compare_walk.sort()
res_walk.sort()
self.assertEqual(len(compare_walk), len(res_walk))
for idx in range(0,len(compare_walk)):
compfile = MASTFile(compare_walk[idx])
myfile = MASTFile(res_walk[idx])
self.assertEqual(compfile.data, myfile.data)
def test_softlink_wavefunction_file(self):
import subprocess
myvc = VaspChecker(name="files")
myvc.softlink_wavefunction_file("childdir")
myfiles = dirutil.walkfiles("childdir")
print myfiles
# self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir", stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/WAVECAR" in listres)
def test_softlink_a_file_emptyparentfile(self):
allowed=dict()
allowed['name']=(str,"","Directory name")
mybc=BaseChecker(allowed,name='files')
mybc.softlink_a_file('childdir','emptyfile')
myfiles=dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme=subprocess.Popen("ls -l childdir",stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
listres=listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/emptyfile" in listres)
def test_softlink_a_file_child_file_exists(self):
allowed=dict()
allowed['name']=(str,"","Directory name")
shutil.copy('files/another_alphatest','childdir/alphatest')
mybc=BaseChecker(allowed,name='files')
mybc.softlink_a_file('childdir','alphatest')
myfiles=dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme=subprocess.Popen("ls -l childdir",stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
listres=listme.communicate()[0]
listme.wait()
print listres
self.assertFalse("files/alphatest" in listres)
self.assertTrue("childdir/alphatest" in myfiles)
def test_softlink_wavefunction_file(self):
import subprocess
myvc = VaspChecker(name="files")
myvc.softlink_wavefunction_file("childdir")
myfiles = dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/WAVECAR" in listres)
def test_softlink_a_file_emptyparentfile(self):
allowed = dict()
allowed['name'] = (str, "", "Directory name")
mybc = BaseChecker(allowed, name='files')
mybc.softlink_a_file('childdir', 'emptyfile')
myfiles = dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/emptyfile" in listres)
def test_softlink_a_file_child_file_exists(self):
allowed = dict()
allowed['name'] = (str, "", "Directory name")
shutil.copy('files/another_alphatest', 'childdir/alphatest')
mybc = BaseChecker(allowed, name='files')
mybc.softlink_a_file('childdir', 'alphatest')
myfiles = dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertFalse("files/alphatest" in listres)
self.assertTrue("childdir/alphatest" in myfiles)
def test_softlink_a_file_child_softlink_exists(self):
print "CURDIR: ", os.getcwd()
allowed=dict()
allowed['name']=(str,"","Directory name")
os.chdir("childdir")
linkme=subprocess.Popen("ln -s ../files/another_alphatest alphatest",shell=True)
linkme.wait()
os.chdir(testdir)
mybc=BaseChecker(allowed,name='files')
mybc.softlink_a_file('childdir','alphatest')
myfiles=dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme=subprocess.Popen("ls -l childdir",stdout=subprocess.PIPE, stderr=subprocess.PIPE, shell=True)
listres=listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/another_alphatest" in listres)
self.assertTrue("childdir/alphatest" in myfiles)
def combine_dynamical_matrix_files(self, mydir=""):
"""Combine dynamical matrix files into one file.
The subfiles should be in subfolders under
the top directory.
Args:
mydir <str>: top directory for DYNMAT files.
Use ingredient directory if null.
Returns:
Creates a single DYNMAT file
"""
if mydir == "":
mydir = self.keywords['name']
dynmatlist = dirutil.walkfiles(mydir, 2, 5, "*DYNMAT*") #start one level below
if len(dynmatlist) == 0:
raise MASTError("pmgextend combine_dynmats", "No DYNMATs found under " + mydir)
totnumdisp=0
largedyn=dict()
largedyn['atoms'] = dict()
for onedynmat in dynmatlist:
dyndir = os.path.dirname(onedynmat)
onedyn = self.read_my_dynamical_matrix_file(dyndir)
totnumdisp = totnumdisp + onedyn['numdisp']
for atom in onedyn['atoms'].keys():
if not atom in largedyn['atoms'].keys():
largedyn['atoms'][atom]=dict()
mydisp=1 #start at 1
for disp in onedyn['atoms'][atom].keys():
if disp in largedyn['atoms'][atom].keys():
mydisp=mydisp + 1 #increment
largedyn['atoms'][atom][mydisp]=dict()
largedyn['atoms'][atom][mydisp]['displine'] = str(onedyn['atoms'][atom][disp]['displine'])
largedyn['atoms'][atom][mydisp]['dynmat']=list(onedyn['atoms'][atom][disp]['dynmat'])
largedyn['numspec'] = onedyn['numspec'] #should all be the same
largedyn['numatoms'] = onedyn['numatoms']
largedyn['massline'] = onedyn['massline']
largedyn['numdisp'] = totnumdisp
self.write_my_dynamical_matrix_file(largedyn, mydir, "DYNMAT_combined")
self.write_my_dynamical_matrix_file(largedyn, mydir, "DYNMAT")
def test_softlink_a_file_child_softlink_exists(self):
print "CURDIR: ", os.getcwd()
allowed = dict()
allowed['name'] = (str, "", "Directory name")
os.chdir("childdir")
linkme = subprocess.Popen("ln -s ../files/another_alphatest alphatest",
shell=True)
linkme.wait()
os.chdir(testdir)
mybc = BaseChecker(allowed, name='files')
mybc.softlink_a_file('childdir', 'alphatest')
myfiles = dirutil.walkfiles("childdir")
print myfiles
#self.assertTrue("childdir/CHGCAR" in myfiles)
listme = subprocess.Popen("ls -l childdir",
stdout=subprocess.PIPE,
stderr=subprocess.PIPE,
shell=True)
listres = listme.communicate()[0]
listme.wait()
print listres
self.assertTrue("files/another_alphatest" in listres)
self.assertTrue("childdir/alphatest" in myfiles)
def combine_displacement_files(self, mydir=""):
"""Combine displacement files (here XDATCARs) into one file.
Args:
mydir <str>: top directory for DYNMAT files.
Use ingredient directory if null.
"""
if mydir == "":
mydir = self.keywords['name']
largexdat=dict()
xdatlist = dirutil.walkfiles(mydir, 2, 5, "*XDATCAR*") #start one level below
if len(xdatlist) == 0:
raise MASTError("pmgextend combine_displacements", "No XDATCARs found under " + mydir)
kfgct=1 # skip config 1 until the end
largexdat['configs']=dict()
xdatlist.sort() #get them in order
for onexdatmat in xdatlist:
xdatdir = os.path.dirname(onexdatmat)
onexdat = self.read_my_displacement_file(xdatdir)
for kfg in onexdat['configs'].keys():
if kfg == 1: #skip config 1 until the end
pass
else:
kfgct = kfgct + 1 #start at 2
largexdat['configs'][kfgct] = onexdat['configs'][kfg]
largexdat['configs'][1] = onexdat['configs'][1] #get one of the first configs (the first should be the same for all the XDATCARs)
largexdat['descline'] = onexdat['descline'] #should all be the same
largexdat['specline'] = onexdat['specline']
largexdat['scale'] = onexdat['scale']
largexdat['latta'] = onexdat['latta']
largexdat['lattb'] = onexdat['lattb']
largexdat['lattc'] = onexdat['lattc']
largexdat['numline'] = onexdat['numline']
largexdat['numatoms'] = onexdat['numatoms']
largexdat['type'] = onexdat['type']
self.write_my_displacement_file(largexdat, mydir, "XDATCAR_combined")
self.write_my_displacement_file(largexdat, mydir, "XDATCAR")
def parse_ingredients_section(self, section_name, section_content,
options):
"""Parses the ingredients section and populates the options.
Section takes the form of:
$ingredients
begin ingredients_global
mast_kpoints 3x3x3
mast_xc pbe
end
begin singlepoint
encut 400
end
begin optimize
encut 300
ibrion 2
end
$end
mast_kpoints are parsed out as a 3 index list of integers.
Everything else is parsed out as a string.
Anything in ingredients_global is then appended onto each
individual ingredient.
"""
global_dict = dict()
ingredients_dict = dict()
for line in section_content:
if (line.startswith('begin')):
# Each ingredient section starts with "begin".
# Check for this line, and initialize the individual
# ingredient dictionary
ingredient_name = line.split()[1]
ingredient_dict = dict()
elif (not (line == 'end')):
opt = line.split()
# print opt
if (opt[0] == 'mast_kpoints'):
try:
kpts = map(int, opt[1].split('x'))
if len(opt) > 2:
kpts.append(opt[2])
except ValueError:
kpts = opt[1:]
# Second option after mast_kpoints tells where to
# center the k-point mesh.
# If it's there, we append it onto the k-point grid list.
ingredient_dict[opt[0]] = kpts
elif (opt[0] == 'mast_pp_setup'):
psp_dict = dict()
for key in opt[1:]:
key = key.split('=')
ref = key[0].title()
val = str().join(key[1][0].upper() + key[1][1:])
psp_dict[ref] = val
ingredient_dict[opt[0]] = psp_dict
#elif (opt[0] == 'mast_exec'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_strain'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'ptemp'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'rwigs'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_setmagmom'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
elif (opt[0] == 'mast_coordinates'):
shortsplit = opt[1].split(",")
filesplit = list()
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
for shortname in shortsplit:
for fullfile in myfiles:
if shortname.strip() in os.path.basename(fullfile):
filesplit.append(fullfile)
if not (len(filesplit) == len(shortsplit)):
raise MASTError(
self.__class__.__name__,
"Not all files given by %s were found in %s." %
(shortsplit, origindir))
ingredient_dict[opt[0]] = filesplit
else:
ingredient_dict[opt[0]] = ' '.join(
opt[1:]) #preserve whole line
#ingredient_dict[opt[0]] = opt[1] #old behavior took only the first part
if (opt[0] == 'mast_program') and (opt[1] == 'vasp'
or opt[1] == 'vasp_neb'):
if os.getenv('VASP_PSP_DIR') == None:
raise MASTError(
self.__class__.__name__,
"Input file specifies program vasp, but no POTCAR directory is set in environment variable VASP_PSP_DIR"
)
elif ('end' in line):
# Each ingredient section ends with "end", if present finish
# that current section and assign
# the neccessary element in the ingredients dictionary and
# create the global dictionary
if (ingredient_name == 'ingredients_global'):
global_dict = ingredient_dict
else:
ingredients_dict[ingredient_name] = ingredient_dict
# Each value in ingredients_dict is a dictionary containing the relevant
# ingredient and option(s).
for ing_key, ing_value in ingredients_dict.items():
options.set_item(section_name, ing_key, ing_value)
options.set_item(section_name, 'global', global_dict)
def parse_structure_section(self, section_name, section_content, options):
"""Parses the structure section and populate the options.
Does not create the structure.
Format is along the lines of:
coord_type fractional
begin coordinates
Ga 0.000000 0.000000 0.000000
Ga 0.500000 0.500000 0.000000
Ga 0.000000 0.500000 0.500000
Ga 0.500000 0.000000 0.500000
As 0.250000 0.250000 0.250000
As 0.750000 0.750000 0.250000
As 0.250000 0.750000 0.750000
As 0.750000 0.250000 0.750000
end
begin lattice
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 2.0
end
Note that coord_type will default to "cartesian" if not specified.
"""
# Initialize with default values
structure_dict = STRUCTURE_KEYWORDS.copy()
subsection_dict = dict()
for myline in section_content:
line = myline.split()
if (line[0] in structure_dict):
structure_dict[line[0]] = line[1]
elif ('begin' in line[0]):
subsection = line[1]
subsection_list = list()
elif ('end' not in line):
lsplit = myline.split()
lineval = list()
for lval in lsplit:
lval.strip()
if len(lval) > 0:
lineval.append(lval)
subsection_list.append(lineval)
elif ('end' in line):
subsection_dict[subsection] = subsection_list
# GRJ: Since we lowercase the whole input file, and filenames may not
# conform to this, we examine the current directory for any files that
# may match and use that. If there are multiple matches, we'll throw
# an error.
if (structure_dict['posfile']
is not None): # Do we have a geometry file?
# TTM for issue #423
posfiletry = os.path.join(os.getcwd(), structure_dict['posfile'])
if os.path.isfile(posfiletry):
self.logger.info("Using posfile %s in directory %s" %
(structure_dict['posfile'], os.getcwd()))
else:
# First build a list of likely files
origindir = os.path.dirname(self.keywords['inputfile'])
if origindir == "":
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
file_list = list()
for myfile in myfiles:
if structure_dict['posfile'] in myfile:
file_list.append(myfile)
if (len(file_list) > 1):
# If we have multiple files with the same name, but different capitalization, throw an error here
self.logger.warning(
'Found multiple files with the name %s' %
structure_dict['posfile'])
self.logger.warning('Found the files:')
for file in file_list:
self.logger.warning(file)
error = 'Found ambiguous file names'
raise MASTError(self.__class__.__name__, error)
elif len(file_list) == 0:
raise MASTError(
self.__class__.__name__,
"No structure file %s found in %s" %
(structure_dict['posfile'], origindir))
else:
structure_dict['posfile'] = file_list[0]
# print 'in InputParser.parse_structure_section:', subsection_dict
# TM
element_map = dict()
atom_list = list()
for key, value in subsection_dict.items():
if (key == 'coordinates'):
value = np.array(value)
# Here we use .title() to re-capitalize the first letter of all
# the atomic symbols to comply with what
# pymatgen needs
atom_list = [val.title() for val in value[:, 0]]
structure_dict['atom_list'] = atom_list
coordinates = np.array(value[:, 1:], dtype='float')
structure_dict['coordinates'] = coordinates
if (key == 'lattice'):
#print "VALUE: ", value
lattice = np.array(value, dtype='float')
structure_dict['lattice'] = lattice
if (key == 'elementmap'):
for elline in value:
elkey = elline[0].strip().upper() #all caps
elname = elline[1].strip().title() #Title case
element_map[elkey] = elname
structure_dict['element_map'] = element_map
if len(element_map) > 0 and len(atom_list) > 0:
new_atom_list = list()
for atomval in atom_list:
if atomval.upper() in element_map.keys():
new_atom_list.append(element_map[atomval])
else:
new_atom_list.append(atomval)
structure_dict['atom_list'] = new_atom_list
for key, value in structure_dict.items():
options.set_item(section_name, key, value)
def parse_ingredients_section(self, section_name, section_content, options):
"""Parses the ingredients section and populates the options.
Section takes the form of:
$ingredients
begin ingredients_global
mast_kpoints 3x3x3
mast_xc pbe
end
begin singlepoint
encut 400
end
begin optimize
encut 300
ibrion 2
end
$end
mast_kpoints are parsed out as a 3 index list of integers.
Everything else is parsed out as a string.
Anything in ingredients_global is then appended onto each
individual ingredient.
"""
global_dict = dict()
ingredients_dict = dict()
for line in section_content:
if (line.startswith('begin')):
# Each ingredient section starts with "begin".
# Check for this line, and initialize the individual
# ingredient dictionary
ingredient_name = line.split()[1]
ingredient_dict = dict()
elif (not (line == 'end')):
opt = line.split()
# print opt
if (opt[0] == 'mast_kpoints'):
try:
kpts = map(int, opt[1].split('x'))
if len(opt) > 2:
kpts.append(opt[2])
except ValueError:
kpts = opt[1:]
# Second option after mast_kpoints tells where to
# center the k-point mesh.
# If it's there, we append it onto the k-point grid list.
ingredient_dict[opt[0]] = kpts
elif (opt[0] == 'mast_pp_setup'):
psp_dict = dict()
for key in opt[1:]:
key = key.split('=')
ref = key[0].title()
val = str().join(key[1][0].upper() + key[1][1:])
psp_dict[ref] = val
ingredient_dict[opt[0]] = psp_dict
#elif (opt[0] == 'mast_exec'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_strain'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'ptemp'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'rwigs'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#elif (opt[0] == 'mast_setmagmom'):
# ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
elif (opt[0] == 'mast_coordinates'):
shortsplit = opt[1].split(",")
filesplit=list()
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
for shortname in shortsplit:
for fullfile in myfiles:
if shortname.strip() in os.path.basename(fullfile):
filesplit.append(fullfile)
if not (len(filesplit) == len(shortsplit)):
raise MASTError(self.__class__.__name__, "Not all files given by %s were found in %s." % (shortsplit, origindir))
ingredient_dict[opt[0]] = filesplit
else:
ingredient_dict[opt[0]] = ' '.join(opt[1:]) #preserve whole line
#ingredient_dict[opt[0]] = opt[1] #old behavior took only the first part
if (opt[0] == 'mast_program') and (opt[1] == 'vasp' or opt[1] == 'vasp_neb'):
if os.getenv('VASP_PSP_DIR') == None:
raise MASTError(self.__class__.__name__, "Input file specifies program vasp, but no POTCAR directory is set in environment variable VASP_PSP_DIR")
elif ('end' in line):
# Each ingredient section ends with "end", if present finish
# that current section and assign
# the neccessary element in the ingredients dictionary and
# create the global dictionary
if (ingredient_name == 'ingredients_global'):
global_dict = ingredient_dict
else:
ingredients_dict[ingredient_name] = ingredient_dict
# Each value in ingredients_dict is a dictionary containing the relevant
# ingredient and option(s).
for ing_key, ing_value in ingredients_dict.items():
options.set_item(section_name, ing_key, ing_value)
options.set_item(section_name, 'global', global_dict)
def parse_structure_section(self, section_name, section_content, options):
"""Parses the structure section and populate the options.
Does not create the structure.
Format is along the lines of:
coord_type fractional
begin coordinates
Ga 0.000000 0.000000 0.000000
Ga 0.500000 0.500000 0.000000
Ga 0.000000 0.500000 0.500000
Ga 0.500000 0.000000 0.500000
As 0.250000 0.250000 0.250000
As 0.750000 0.750000 0.250000
As 0.250000 0.750000 0.750000
As 0.750000 0.250000 0.750000
end
begin lattice
2.0 0.0 0.0
0.0 2.0 0.0
0.0 0.0 2.0
end
Note that coord_type will default to "cartesian" if not specified.
"""
# Initialize with default values
structure_dict = STRUCTURE_KEYWORDS.copy()
subsection_dict = dict()
for myline in section_content:
line = myline.split()
if (line[0] in structure_dict):
structure_dict[line[0]] = line[1]
elif ('begin' in line[0]):
subsection = line[1]
subsection_list = list()
elif ('end' not in line):
lsplit = myline.split()
lineval = list()
for lval in lsplit:
lval.strip()
if len(lval) > 0:
lineval.append(lval)
subsection_list.append(lineval)
elif ('end' in line):
subsection_dict[subsection] = subsection_list
# GRJ: Since we lowercase the whole input file, and filenames may not
# conform to this, we examine the current directory for any files that
# may match and use that. If there are multiple matches, we'll throw
# an error.
if (structure_dict['posfile'] is not None): # Do we have a geometry file?
# TTM for issue #423
posfiletry = os.path.join(os.getcwd(), structure_dict['posfile'])
if os.path.isfile(posfiletry):
self.logger.info("Using posfile %s in directory %s" % (structure_dict['posfile'], os.getcwd()))
else:
# First build a list of likely files
origindir = os.path.dirname(self.keywords['inputfile'])
if origindir == "":
origindir = os.getcwd()
metatry = os.path.join(os.getcwd(), 'metadata.txt')
if os.path.isfile(metatry):
myrecipemeta = Metadata(metafile=metatry)
origindir = myrecipemeta.search_data('origin_dir')[1]
myfiles = dirutil.walkfiles(origindir)
file_list=list()
for myfile in myfiles:
if structure_dict['posfile'] in myfile:
file_list.append(myfile)
if (len(file_list) > 1):
# If we have multiple files with the same name, but different capitalization, throw an error here
self.logger.warning('Found multiple files with the name %s' % structure_dict['posfile'])
self.logger.warning('Found the files:')
for file in file_list:
self.logger.warning(file)
error='Found ambiguous file names'
raise MASTError(self.__class__.__name__, error)
elif len(file_list) == 0:
raise MASTError(self.__class__.__name__, "No structure file %s found in %s" % (structure_dict['posfile'], origindir))
else:
structure_dict['posfile'] = file_list[0]
# print 'in InputParser.parse_structure_section:', subsection_dict
# TM
element_map = dict()
atom_list = list()
for key, value in subsection_dict.items():
if (key == 'coordinates'):
value = np.array(value)
# Here we use .title() to re-capitalize the first letter of all
# the atomic symbols to comply with what
# pymatgen needs
atom_list = [val.title() for val in value[:, 0]]
structure_dict['atom_list'] = atom_list
coordinates = np.array(value[:, 1:], dtype='float')
structure_dict['coordinates'] = coordinates
if (key == 'lattice'):
#print "VALUE: ", value
lattice = np.array(value, dtype='float')
structure_dict['lattice'] = lattice
if (key == 'elementmap'):
for elline in value:
elkey = elline[0].strip().upper() #all caps
elname = elline[1].strip().title() #Title case
element_map[elkey]=elname
structure_dict['element_map'] = element_map
if len(element_map) > 0 and len(atom_list) > 0:
new_atom_list = list()
for atomval in atom_list:
if atomval.upper() in element_map.keys():
new_atom_list.append(element_map[atomval])
else:
new_atom_list.append(atomval)
structure_dict['atom_list'] = new_atom_list
for key, value in structure_dict.items():
options.set_item(section_name, key, value)